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                <title>Peak detection - Targeted peak detection</title>
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                <h1>Targeted peak detection</h1>

                <h2>Description</h2>

                <p>
                        This algorithm opens a csv file with a list of peaks and search each peak in the selected raw data file.
                        The most crucial parameters are "m/z tolerance" and "RT tolerance" which define the window where
                        the algorithm should find the new peak. It is centered in the m/z average and retention time average of
                        the source peak list. Once the best candidate is found inside the window, its shape in RT direction is also
                        checked.
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                <p>
                        The csv file should have three columns. The first column should contain the expected M/Z,
                        the second column the expected RT and the third the peak name.
                        Each peak should be in a different row.
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                <h4>Method parameters</h4>

                <dl>
                        <dt>Name suffix</dt>
                        <dd>Suffix to be added to the peak list name.</dd>

                        <dt>Peak list file</dt>
                        <dd>Path of the csv file containing the list of peaks to be detected.</dd>

                        <dt>Field separator</dt>
                        <dd>Character(s) used to separate fields in the peak list file.</dd>

                        <dt>Ignore first line</dt>
                        <dd>Check to ignore the first line of  peak list file.</dd>

                        <dt>Intensity tolerance</dt>
                        <dd>This value sets the maximum allowed deviation from expected shape of a peak in chromatographic direction.</dd>
                        
                        <dt>Noise level</dt>
                        <dd>The minimum intensity level for a data point to be considered part of a chromatogram. All data points below this intensity level are ignored.</dd>

                        <dt>MZ Tolerance </dt>
                        <dd>Maximum allowed m/z difference to find the peak</dd>

                        <dt>RT tolerance</dt>
                        <dd>Maximum allowed retention time difference to find the peak</dd>

                </dl>


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